Imputation Report For Cohort: AdDIT_cohort

Per chromosome imputation report for cohort AdDIT_cohort.

Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC2

UPLOADED 8.4.2021

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 12656029 73.301
0.1 1220330 7.068
0.2 812833 4.708
0.3 618189 3.580
0.4 497862 2.883
0.5 407006 2.357
0.6 350434 2.030
0.7 291717 1.690
0.8 244550 1.416
0.9 166949 0.967
Total 17265899 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.3 751476 4.352
0.4 831520 4.816
0.5 1066702 6.178
0.6 1525605 8.836
0.7 2108921 12.214
0.8 2793714 16.181
0.9 8160726 47.265
1.0 27235 0.158
Total 17265899 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 966467 73.7471
0.1 90429 6.9003
0.2 58268 4.4462
0.3 45460 3.4689
0.4 37556 2.8657
0.5 30979 2.3639
0.6 26905 2.0530
0.7 21703 1.6561
0.8 18811 1.4354
0.9 13938 1.0636
Total 1310516

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 59290 4.5242
0.4 64654 4.9335
0.5 82333 6.2825
0.6 118554 9.0464
0.7 164713 12.5686
0.8 211407 16.1316
0.9 607677 46.3693
1.0 1888 0.1441
Total 1310516

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1062941 73.9511
0.1 100912 7.0207
0.2 65456 4.5539
0.3 49642 3.4537
0.4 38704 2.6927
0.5 33285 2.3157
0.6 28757 2.0007
0.7 23484 1.6338
0.8 20062 1.3958
0.9 14114 0.9819
Total 1437357

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 61380 4.2703
0.4 67083 4.6671
0.5 86577 6.0233
0.6 124233 8.6432
0.7 174506 12.1408
0.8 234186 16.2928
0.9 687424 47.8256
1.0 1968 0.1369
Total 1437357

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 891117 73.3682
0.1 87680 7.2189
0.2 55340 4.5563
0.3 42641 3.5108
0.4 35907 2.9563
0.5 29177 2.4022
0.6 24085 1.9830
0.7 20728 1.7066
0.8 16616 1.3680
0.9 11291 0.9296
Total 1214582

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 49880 4.1068
0.4 55355 4.5575
0.5 70628 5.8150
0.6 103762 8.5430
0.7 147390 12.1350
0.8 193240 15.9100
0.9 591545 48.7036
1.0 2782 0.2290
Total 1214582

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 880023 72.6617
0.1 82339 6.7986
0.2 61749 5.0985
0.3 44563 3.6795
0.4 34021 2.8090
0.5 27984 2.3106
0.6 24659 2.0360
0.7 21830 1.8025
0.8 20015 1.6526
0.9 13941 1.1511
Total 1211124

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 49972 4.1261
0.4 54395 4.4913
0.5 70549 5.8251
0.6 100328 8.2839
0.7 143584 11.8554
0.8 193538 15.9800
0.9 596919 49.2864
1.0 1839 0.1518
Total 1211124

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 809027 73.4822
0.1 76612 6.9585
0.2 52758 4.7919
0.3 40736 3.7000
0.4 31654 2.8751
0.5 24054 2.1848
0.6 22903 2.0802
0.7 18065 1.6408
0.8 15241 1.3843
0.9 9934 0.9023
Total 1100984

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 45191 4.1046
0.4 49068 4.4567
0.5 62668 5.6920
0.6 92455 8.3975
0.7 132595 12.0433
0.8 178899 16.2490
0.9 538678 48.9270
1.0 1430 0.1299
Total 1100984

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 789150 72.6259
0.1 80092 7.3709
0.2 52699 4.8499
0.3 40865 3.7608
0.4 32870 3.0250
0.5 26257 2.4164
0.6 22716 2.0906
0.7 16932 1.5583
0.8 15155 1.3947
0.9 9860 0.9074
Total 1086596

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 41971 3.8626
0.4 45608 4.1973
0.5 58154 5.3519
0.6 84972 7.8200
0.7 120042 11.0475
0.8 164229 15.1141
0.9 568019 52.2751
1.0 3601 0.3314
Total 1086596

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 709402 72.9813
0.1 69801 7.1809
0.2 47707 4.9080
0.3 35465 3.6485
0.4 28955 2.9788
0.5 23916 2.4604
0.6 18840 1.9382
0.7 16489 1.6963
0.8 12451 1.2809
0.9 9006 0.9265
Total 972032

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 40998 4.2178
0.4 45179 4.6479
0.5 58368 6.0047
0.6 84104 8.6524
0.7 118431 12.1839
0.8 158943 16.3516
0.9 464964 47.8342
1.0 1045 0.1075
Total 972032

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 700630 73.8905
0.1 64522 6.8047
0.2 44128 4.6539
0.3 32399 3.4169
0.4 27787 2.9305
0.5 21621 2.2802
0.6 19308 2.0363
0.7 15456 1.6300
0.8 13494 1.4231
0.9 8856 0.9340
Total 948201

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 39596 4.1759
0.4 43975 4.6377
0.5 55405 5.8432
0.6 79921 8.4287
0.7 111698 11.7800
0.8 151444 15.9717
0.9 464502 48.9877
1.0 1660 0.1751
Total 948201

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 530147 73.3251
0.1 53790 7.4397
0.2 34107 4.7174
0.3 24677 3.4131
0.4 21010 2.9059
0.5 15506 2.1446
0.6 14614 2.0213
0.7 12050 1.6666
0.8 9964 1.3781
0.9 7144 0.9881
Total 723009

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 29858 4.1297
0.4 33239 4.5973
0.5 43470 6.0124
0.6 62820 8.6887
0.7 89398 12.3647
0.8 120551 16.6735
0.9 342637 47.3904
1.0 1036 0.1433
Total 723009

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 611955 72.9375
0.1 60678 7.2321
0.2 39895 4.7550
0.3 28872 3.4412
0.4 24833 2.9598
0.5 20733 2.4711
0.6 16759 1.9975
0.7 14541 1.7331
0.8 12646 1.5072
0.9 8101 0.9655
Total 839013

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 34267 4.0842
0.4 38216 4.5549
0.5 48690 5.8032
0.6 69787 8.3177
0.7 98642 11.7569
0.8 135065 16.0981
0.9 413182 49.2462
1.0 1164 0.1387
Total 839013

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 612997 73.1761
0.1 58074 6.9325
0.2 36815 4.3948
0.3 31125 3.7155
0.4 23516 2.8072
0.5 20691 2.4700
0.6 18653 2.2267
0.7 14201 1.6952
0.8 12440 1.4850
0.9 9189 1.0969
Total 837701

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 33534 4.0031
0.4 36468 4.3533
0.5 46939 5.6033
0.6 70533 8.4198
0.7 101549 12.1223
0.8 135487 16.1737
0.9 410930 49.0545
1.0 2261 0.2699
Total 837701

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 584684 73.1803
0.1 56466 7.0674
0.2 36008 4.5068
0.3 30383 3.8028
0.4 23212 2.9053
0.5 18890 2.3643
0.6 15974 1.9993
0.7 12706 1.5903
0.8 12535 1.5689
0.9 8106 1.0146
Total 798964

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 33738 4.2227
0.4 37108 4.6445
0.5 47580 5.9552
0.6 68860 8.6187
0.7 96242 12.0458
0.8 129496 16.2080
0.9 384678 48.1471
1.0 1262 0.1580
Total 798964

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 437431 72.1844
0.1 43121 7.1158
0.2 27958 4.6136
0.3 22486 3.7106
0.4 17350 2.8631
0.5 15918 2.6268
0.6 12671 2.0910
0.7 11187 1.8461
0.8 9878 1.6301
0.9 7991 1.3187
Total 605991

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 24473 4.0385
0.4 26689 4.4042
0.5 34626 5.7139
0.6 51729 8.5363
0.7 74057 12.2208
0.8 97783 16.1360
0.9 295801 48.8128
1.0 833 0.1375
Total 605991

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 398809 73.5703
0.1 38977 7.1903
0.2 26026 4.8011
0.3 18193 3.3562
0.4 15213 2.8064
0.5 11912 2.1975
0.6 10163 1.8748
0.7 8998 1.6599
0.8 8154 1.5042
0.9 5634 1.0393
Total 542079

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 22566 4.1629
0.4 25123 4.6346
0.5 32842 6.0585
0.6 48039 8.8620
0.7 65764 12.1318
0.8 87489 16.1395
0.9 259805 47.9275
1.0 451 0.0832
Total 542079

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 346726 73.1712
0.1 33035 6.9715
0.2 22326 4.7116
0.3 16928 3.5724
0.4 14676 3.0971
0.5 11407 2.4073
0.6 9081 1.9164
0.7 7902 1.6676
0.8 6452 1.3616
0.9 5323 1.1233
Total 473856

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 22708 4.7922
0.4 26108 5.5097
0.5 32786 6.9190
0.6 44968 9.4898
0.7 59508 12.5582
0.8 78155 16.4934
0.9 209179 44.1440
1.0 444 0.0937
Total 473856

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 391267 74.0213
0.1 37989 7.1869
0.2 23002 4.3516
0.3 18676 3.5332
0.4 14486 2.7405
0.5 12304 2.3277
0.6 10735 2.0309
0.7 9284 1.7564
0.8 6816 1.2895
0.9 4028 0.7620
Total 528587

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 25517 4.8274
0.4 28407 5.3741
0.5 36284 6.8643
0.6 52209 9.8771
0.7 70135 13.2684
0.8 91425 17.2961
0.9 224216 42.4180
1.0 394 0.0745
Total 528587

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 331414 73.4976
0.1 30520 6.7684
0.2 23106 5.1242
0.3 15653 3.4714
0.4 13167 2.9200
0.5 11149 2.4725
0.6 8850 1.9627
0.7 8258 1.8314
0.8 5626 1.2477
0.9 3175 0.7041
Total 450918

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 23205 5.1462
0.4 26222 5.8152
0.5 35251 7.8176
0.6 47373 10.5059
0.7 59987 13.3033
0.8 75212 16.6798
0.9 183254 40.6402
1.0 414 0.0918
Total 450918

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 349865 72.9769
0.1 34517 7.1998
0.2 23288 4.8575
0.3 17634 3.6782
0.4 14136 2.9486
0.5 10703 2.2325
0.6 9768 2.0375
0.7 8042 1.6774
0.8 6556 1.3675
0.9 4910 1.0242
Total 479419

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 21188 4.4195
0.4 23890 4.9831
0.5 32012 6.6772
0.6 45178 9.4235
0.7 61083 12.7410
0.8 80331 16.7559
0.9 215268 44.9018
1.0 469 0.0978
Total 479419

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 268904 72.8196
0.1 29275 7.9277
0.2 18717 5.0686
0.3 13440 3.6396
0.4 9669 2.6184
0.5 8856 2.3982
0.6 6920 1.8739
0.7 6206 1.6806
0.8 4604 1.2468
0.9 2683 0.7266
Total 369274

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 19544 5.2925
0.4 23128 6.2631
0.5 28493 7.7160
0.6 38990 10.5586
0.7 48736 13.1978
0.8 61386 16.6234
0.9 148533 40.2230
1.0 464 0.1257
Total 369274

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 275018 73.3595
0.1 26906 7.1770
0.2 18262 4.8713
0.3 13518 3.6058
0.4 11255 3.0022
0.5 8610 2.2967
0.6 7984 2.1297
0.7 5790 1.5444
0.8 4643 1.2385
0.9 2905 0.7749
Total 374891

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 17139 4.5717
0.4 19556 5.2164
0.5 25659 6.8444
0.6 36383 9.7050
0.7 47916 12.7813
0.8 62547 16.6840
0.9 165402 44.1200
1.0 289 0.0771
Total 374891

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 164583 72.1441
0.1 15793 6.9228
0.2 10466 4.5877
0.3 9211 4.0376
0.4 7017 3.0759
0.5 6139 2.6910
0.6 4857 2.1290
0.7 4435 1.9441
0.8 3999 1.7529
0.9 1631 0.7149
Total 228131

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 11224 4.9200
0.4 12183 5.3404
0.5 15785 6.9193
0.6 22366 9.8040
0.7 28606 12.5393
0.8 37683 16.5181
0.9 100079 43.8691
1.0 205 0.0899
Total 228131

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 159777 73.1074
0.1 15525 7.1036
0.2 10987 5.0272
0.3 7860 3.5964
0.4 6734 3.0812
0.5 5084 2.3262
0.6 4487 2.0531
0.7 4002 1.8312
0.8 2644 1.2098
0.9 1451 0.6639
Total 218551

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 11663 5.3365
0.4 13065 5.9780
0.5 16314 7.4646
0.6 21998 10.0654
0.7 28113 12.8634
0.8 35011 16.0196
0.9 92228 42.1998
1.0 159 0.0728
Total 218551

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome X

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 383695 74.6310
0.1 33277 6.4726
0.2 23765 4.6224
0.3 17762 3.4548
0.4 14134 2.7491
0.5 11831 2.3012
0.6 10745 2.0900
0.7 9428 1.8338
0.8 5748 1.1180
0.9 3738 0.7271
Total 514123

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 32574 6.3358
0.4 36801 7.1580
0.5 45289 8.8090
0.6 56043 10.9007
0.7 66226 12.8814
0.8 80207 15.6007
0.9 195806 38.0854
1.0 1177 0.2289
Total 514123

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering